Summary Structural details Experimental details Functional details Sequence Neighbor History Downloads

3A8M

Crystal structure of Nitrile Hydratase mutant Y72F complexed with Trimethylacetonitrile

Functional Information from GO Data

Chain	GOid	namespace	contents
A	0003824	molecular_function	catalytic activity
A	0016829	molecular_function	lyase activity
A	0018822	molecular_function	nitrile hydratase activity
A	0046872	molecular_function	metal ion binding
A	0046914	molecular_function	transition metal ion binding
B	0016829	molecular_function	lyase activity
B	0018822	molecular_function	nitrile hydratase activity
B	0046914	molecular_function	transition metal ion binding

Functional Information from PDB Data

site_id	AC1
Number of Residues	5
Details	BINDING SITE FOR RESIDUE FE A 300

Chain	Residue
A	CYS109
A	CSD112
A	SER113
A	CSD114
A	HOH290

site_id	AC2
Number of Residues	7
Details	BINDING SITE FOR RESIDUE MG B 301

Chain	Residue
B	HOH395
B	HOH395
B	HOH400
B	HOH255
B	HOH364
B	HOH366
B	HOH393

site_id	AC3
Number of Residues	6
Details	BINDING SITE FOR RESIDUE MG B 302

Chain	Residue
B	HOH278
B	HOH299
B	HOH363
B	HOH374
B	HOH411
B	HOH422

site_id	AC4
Number of Residues	6
Details	BINDING SITE FOR RESIDUE MG B 303

Chain	Residue
B	HOH232
B	HOH264
B	HOH284
B	HOH300
B	HOH375
B	HOH379

site_id	AC5
Number of Residues	5
Details	BINDING SITE FOR RESIDUE TAN B 213

Chain	Residue
A	CSD112
A	SER113
B	TYR37
B	MET40
B	ARG56

Functional Information from SwissProt/UniProt

site_id	SWS_FT_FI1
Number of Residues	1
Details	Active site: {"description":"Nucleophile","evidences":[{"source":"PubMed","id":"18948265","evidenceCode":"ECO:0000269"},{"source":"PubMed","id":"26333053","evidenceCode":"ECO:0000269"}]}

Chain

Residue

Details

site_id	SWS_FT_FI2
Number of Residues	2
Details	Binding site: {"evidences":[{"source":"PubMed","id":"16636455","evidenceCode":"ECO:0000269"},{"source":"PubMed","id":"17716629","evidenceCode":"ECO:0000269"},{"source":"PubMed","id":"18948265","evidenceCode":"ECO:0000269"},{"source":"PubMed","id":"20221653","evidenceCode":"ECO:0000269"},{"source":"PubMed","id":"26333053","evidenceCode":"ECO:0000269"},{"source":"PubMed","id":"9368004","evidenceCode":"ECO:0000269"},{"source":"PubMed","id":"9586994","evidenceCode":"ECO:0000269"},{"source":"Reference","evidenceCode":"ECO:0000269","citation":{"citationType":"submission","publicationDate":"JUL-2005","submissionDatabase":"PDB data bank","title":"Photo-activation state of Fe-type NHase in anaerobic and aerobic conditions.","authors":["Kawano Y.","Hashimoto K.","Odaka M.","Nakayama H.","Takio K.","Endo I.","Kamiya N."]}},{"source":"Reference","evidenceCode":"ECO:0000269","citation":{"citationType":"submission","publicationDate":"DEC-2014","submissionDatabase":"PDB data bank","title":"Reaction intermediate of nitrile hydratase determined by time-resolved crystallography reveals the cysteine-sulfenic acid ligand to be a catalytic nucleophile.","authors":["Yamanaka Y.","Hashimoto K.","Noguchi K.","Yohda M.","Odaka M."]}},{"source":"PDB","id":"2AHJ","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"2CYZ","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"2CZ0","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"2CZ1","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"2CZ6","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"2CZ7","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"2D0Q","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"2QDY","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"2ZPB","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"2ZPE","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"2ZPF","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"2ZPG","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"2ZPH","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"2ZPI","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"3A8G","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"3A8H","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"3A8L","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"3A8M","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"3A8O","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"3WVD","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"3WVE","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"3X20","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"3X24","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"3X25","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"3X26","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"3X28","evidenceCode":"ECO:0007744"}]}

Chain

Residue

Details

site_id	SWS_FT_FI3
Number of Residues	1
Details	Binding site: {"evidences":[{"source":"PubMed","id":"16636455","evidenceCode":"ECO:0000269"},{"source":"PubMed","id":"17716629","evidenceCode":"ECO:0000269"},{"source":"PubMed","id":"18948265","evidenceCode":"ECO:0000269"},{"source":"PubMed","id":"20221653","evidenceCode":"ECO:0000269"},{"source":"PubMed","id":"26333053","evidenceCode":"ECO:0000269"},{"source":"PubMed","id":"9368004","evidenceCode":"ECO:0000269"},{"source":"PubMed","id":"9586994","evidenceCode":"ECO:0000269"},{"source":"Reference","evidenceCode":"ECO:0000269","citation":{"citationType":"submission","publicationDate":"JUL-2005","submissionDatabase":"PDB data bank","title":"Photo-activation state of Fe-type NHase in anaerobic and aerobic conditions.","authors":["Kawano Y.","Hashimoto K.","Odaka M.","Nakayama H.","Takio K.","Endo I.","Kamiya N."]}},{"source":"Reference","evidenceCode":"ECO:0000269","citation":{"citationType":"submission","publicationDate":"DEC-2014","submissionDatabase":"PDB data bank","title":"Reaction intermediate of nitrile hydratase determined by time-resolved crystallography reveals the cysteine-sulfenic acid ligand to be a catalytic nucleophile.","authors":["Yamanaka Y.","Hashimoto K.","Noguchi K.","Yohda M.","Odaka M."]}},{"source":"PDB","id":"2AHJ","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"2CYZ","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"2CZ0","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"2CZ1","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"2CZ6","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"2CZ7","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"2D0Q","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"2QDY","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"2ZPB","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"2ZPE","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"2ZPF","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"2ZPG","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"3A8G","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"3A8H","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"3A8L","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"3A8M","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"3A8O","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"3WVD","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"3WVE","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"3X20","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"3X24","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"3X25","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"3X26","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"3X28","evidenceCode":"ECO:0007744"}]}

Chain

Residue

Details

site_id	SWS_FT_FI4
Number of Residues	1
Details	Binding site: {"evidences":[{"source":"PubMed","id":"16636455","evidenceCode":"ECO:0000269"},{"source":"PubMed","id":"17716629","evidenceCode":"ECO:0000269"},{"source":"PubMed","id":"18948265","evidenceCode":"ECO:0000269"},{"source":"PubMed","id":"20221653","evidenceCode":"ECO:0000269"},{"source":"PubMed","id":"26333053","evidenceCode":"ECO:0000269"},{"source":"PubMed","id":"9368004","evidenceCode":"ECO:0000269"},{"source":"PubMed","id":"9586994","evidenceCode":"ECO:0000269"},{"source":"Reference","evidenceCode":"ECO:0000269","citation":{"citationType":"submission","publicationDate":"JUL-2005","submissionDatabase":"PDB data bank","title":"Photo-activation state of Fe-type NHase in anaerobic and aerobic conditions.","authors":["Kawano Y.","Hashimoto K.","Odaka M.","Nakayama H.","Takio K.","Endo I.","Kamiya N."]}},{"source":"Reference","evidenceCode":"ECO:0000269","citation":{"citationType":"submission","publicationDate":"DEC-2014","submissionDatabase":"PDB data bank","title":"Reaction intermediate of nitrile hydratase determined by time-resolved crystallography reveals the cysteine-sulfenic acid ligand to be a catalytic nucleophile.","authors":["Yamanaka Y.","Hashimoto K.","Noguchi K.","Yohda M.","Odaka M."]}},{"source":"PDB","id":"2AHJ","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"2CYZ","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"2CZ0","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"2CZ1","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"2CZ6","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"2CZ7","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"2D0Q","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"2QDY","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"2ZPB","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"2ZPE","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"2ZPF","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"2ZPG","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"2ZPH","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"2ZPI","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"3A8M","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"3A8O","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"3WVD","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"3WVE","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"3X20","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"3X24","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"3X25","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"3X26","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"3X28","evidenceCode":"ECO:0007744"}]}

Chain

Residue

Details

site_id	SWS_FT_FI5
Number of Residues	1
Details	Modified residue: {"description":"Cysteine sulfinic acid (-SO2H)","evidences":[{"source":"PubMed","id":"16636455","evidenceCode":"ECO:0000269"},{"source":"PubMed","id":"17716629","evidenceCode":"ECO:0000269"},{"source":"PubMed","id":"18948265","evidenceCode":"ECO:0000269"},{"source":"PubMed","id":"20221653","evidenceCode":"ECO:0000269"},{"source":"PubMed","id":"26333053","evidenceCode":"ECO:0000269"},{"source":"PubMed","id":"9368004","evidenceCode":"ECO:0000269"},{"source":"PubMed","id":"9586994","evidenceCode":"ECO:0000269"},{"source":"Reference","evidenceCode":"ECO:0000269","citation":{"citationType":"submission","publicationDate":"JUL-2005","submissionDatabase":"PDB data bank","title":"Photo-activation state of Fe-type NHase in anaerobic and aerobic conditions.","authors":["Kawano Y.","Hashimoto K.","Odaka M.","Nakayama H.","Takio K.","Endo I.","Kamiya N."]}},{"source":"Reference","evidenceCode":"ECO:0000269","citation":{"citationType":"submission","publicationDate":"DEC-2014","submissionDatabase":"PDB data bank","title":"Reaction intermediate of nitrile hydratase determined by time-resolved crystallography reveals the cysteine-sulfenic acid ligand to be a catalytic nucleophile.","authors":["Yamanaka Y.","Hashimoto K.","Noguchi K.","Yohda M.","Odaka M."]}},{"source":"PDB","id":"2AHJ","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"2CYZ","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"2CZ0","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"2CZ1","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"2CZ6","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"2CZ7","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"2D0Q","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"2QDY","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"2ZCF","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"2ZPB","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"2ZPE","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"2ZPF","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"2ZPG","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"2ZPH","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"2ZPI","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"3A8G","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"3A8H","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"3A8L","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"3A8M","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"3A8O","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"3WVD","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"3WVE","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"3X20","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"3X24","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"3X25","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"3X26","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"3X28","evidenceCode":"ECO:0007744"}]}

Chain

Residue

Details

site_id	SWS_FT_FI6
Number of Residues	1
Details	Modified residue: {"description":"Cysteine sulfenic acid (-SOH)","evidences":[{"source":"PubMed","id":"16636455","evidenceCode":"ECO:0000269"},{"source":"PubMed","id":"17716629","evidenceCode":"ECO:0000269"},{"source":"PubMed","id":"18948265","evidenceCode":"ECO:0000269"},{"source":"PubMed","id":"20221653","evidenceCode":"ECO:0000269"},{"source":"PubMed","id":"26333053","evidenceCode":"ECO:0000269"},{"source":"PubMed","id":"9368004","evidenceCode":"ECO:0000269"},{"source":"PubMed","id":"9586994","evidenceCode":"ECO:0000269"},{"source":"Reference","evidenceCode":"ECO:0000269","citation":{"citationType":"submission","publicationDate":"JUL-2005","submissionDatabase":"PDB data bank","title":"Photo-activation state of Fe-type NHase in anaerobic and aerobic conditions.","authors":["Kawano Y.","Hashimoto K.","Odaka M.","Nakayama H.","Takio K.","Endo I.","Kamiya N."]}},{"source":"Reference","evidenceCode":"ECO:0000269","citation":{"citationType":"submission","publicationDate":"DEC-2014","submissionDatabase":"PDB data bank","title":"Reaction intermediate of nitrile hydratase determined by time-resolved crystallography reveals the cysteine-sulfenic acid ligand to be a catalytic nucleophile.","authors":["Yamanaka Y.","Hashimoto K.","Noguchi K.","Yohda M.","Odaka M."]}},{"source":"PDB","id":"2AHJ","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"2CYZ","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"2CZ1","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"2CZ6","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"2CZ7","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"2ZCF","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"2ZPB","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"2ZPE","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"2ZPF","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"2ZPG","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"2ZPH","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"2ZPI","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"3A8G","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"3A8H","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"3A8L","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"3A8O","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"3WVD","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"3WVE","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"3X20","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"3X24","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"3X25","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"3X26","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"3X28","evidenceCode":"ECO:0007744"}]}

Chain

Residue

Details

Catalytic Information from CSA

site_id	MCSA1
Number of Residues	3
Details	M-CSA 57

Chain	Residue	Details
B	ARG56	electrostatic stabiliser, proton acceptor, proton donor
B	PHE72	proton acceptor, proton donor
B	TYR76	increase acidity, increase basicity
A	GLY121	electrofuge, metal ligand, nucleophile, proton acceptor, proton donor

		Sequence (fasta)
		PDBx/mmCIF
		PDBML format (no-atom)
		PDB format (full)
		Validation report (PDF)
		EDMap 2fo-fc (MTZ)